Abstract Bacterial vaginosis (BV), the most common health condition affecting the female reproductive tract, significantly increases the risk of HIV and STI acquisition in women. BV is characterized by changes in the composition of the vaginal bacteria (microbiota), with a reduction in healthy vaginal Lactobacillus species and an increase in gram negative anaerobic bacteria. Women with BV have impaired female reproductive tract mucosal immune responses with increased HIV target cells, as well as decreased epithelial integrity; all which lead to increased HIV risk. Furthermore, a recent study demonstrated that BV-associated bacteria can directly hydrolyze drugs used for HIV prevention, setting up conditions that undermine treatment efficacy. Current antibiotic-based treatments for BV result in failure of treatment or recurrence in the majority of women. Behavioral (sexual behaviors and intravaginal hygiene practices such as intravaginal douching), bacterial factors (microbiome and virome), and host biological factors (mucosal immune responses and inflammation), all may underscore BV recurrence. In this study, we will assess the mechanisms underlying BV recurrence in a unique cohort of reproductive age women (18-45 years) with BV. Reproductive age women with BV will be provided BV treatment and followed longitudinally (one and six months post-BV treatment). Study aims are: 1) To evaluate the role of intravaginal hygiene practices on BV recurrence; 2) To evaluate the role of the vaginal microbiome and virome, and antibiotic metabolism by vaginal bacteria, on BV recurrence; and 3) To evaluate the role of host biological factors on BV recurrence. To our knowledge, this is the first study to mechanistically assess factors that underlie BV recurrence in vivo in a longitudinal study, and specifically, using a comprehensive, multidisciplinary approach (behavioral, microbiological, and immunological). We will use cutting edge technologies to measure these potential mechanisms relative to BV recurrence. Study results will be critical to develop targeted intervention strategies to prevent BV recurrence and thus, better protect women from HIV and STIs.